search

Gleeson-Lab / wxs_pipeline

Starting with BAMs and FASTQs, follow GATK 4.0 Best Practices up to generating a joint-genotyped VCF
1 stars 1 forks source link

Disable PCR Duplicates Marking for Amplicon Sequencing #15

Closed brcopeland closed 2 years ago

brcopeland commented 3 years ago

This protocol can be treated largely the same as WES, but many reads will have the same starting and end positions by design so that PCR duplicate marking is inappropriate. This should be an optional thing to disable in the config file.

brcopeland commented 3 years ago

I have implemented the changes in https://github.com/brcopeland/wxs_pipeline/commit/8ce15f705cc05ce1ede41b3b9f7c8eaca988854e. There is now an option for a sequencing_type of amplicon, which disables duplicate marking, calls variants on the entire genome (instead of on subsetted intervals because these files are small), and disables checking contamination with verifybamid2 due to the low number of informative SNPs encountered. Currently reprocessing some data with this.

shishenyxx commented 3 years ago

Please remember to emphasize this in the document ...-

brcopeland commented 2 years ago

This is documented in the sample types page.